Organic Functional Groups

Table 2.3 (pages 41 AND 42 of text) give the general structures and names of all of the organic functional groups we will use in this course. You will need to memorize and be able to draw Lewis structures for each of these.

Acid/Base Chemistry

For any chemical reaction reaction involving either a strong acid or a strong base, the equilibrium shifts to give the lowest possible concentration of the strong acid or strong base. Put another way, strong acids are very reactive and tend to react with any base present (strong or weak) until all of the strong acid or base is consumed.
For example, assume that HBr is added to a solution containing CH₃COOH (acetic acid) and CH₃COO^-1 (acetate ion). Since HBr is a strong acid, it will react with any base present. In this example, the acetate ion is the base and the following reaction will occur:

CH₃COO^-1 + HBr CH₃COOH + Br^-1

The equilibrium for this reaction will lie as far to the right as possible, giving the lowest concentration of HBr. As a result of this reaction, the concentration of the weak base (CH₃COO^-1) decreases and the concentration of the weak acid (CH₃COOH) increases.

Strong Acids

HCl, HBr, HI, HNO₃, H₂SO₄, HClO₄.

Strong Bases

LiOH, NaOH, KOH

Conjugates

Be able to label acid, base, conjugate acid, and conjugate base in any given reaction. (HW #3).

Buffer

Solution containing both weak acid and weak conjugate base. (See "Supplemental Homework - Chapter 2" for practice problems)

Equations

The following equations will be given. For the first equation, be able to calculate pH given [H⁺] and calculate [H+] given the pH (which is slightly harder).

pH = -log₁₀([H⁺])

pH = pK_a + log₁₀([A^-]/[HA])

The second equation shown is the Henderson-Hasselbalch equation. pK_a values will be available (See Table 2.7 on page 50 of the text for typical values). This equation is typically used to solve buffer problems, where [HA] and [A^-] are the concentrations of the weak acid and its conjugate base, respectively.

Chapter 3

amino acids peptides proteins

Be able to draw standard form of a general "L"-amino acid:     

Given the structure of any amino acid, classify as either
non-polar (neutral), polar (neutral), acidic, or basic.

Using the pK_a values for each amino acid given in Table 3.2 and the structures, be able to draw the predominant structure of any amino acid at any pH value. To do this, you will need to know the structures of both the acid and base forms of the organic functional groups present in amino acids.

Peptides

Given the amino acid sequence, draw the structure of any peptide. Be able to define and identify the N-terminal and C-terminal residues in any peptide. (Ex.: draw the structure and label the peptide bonds in Lys-Gly-Pro ).

Disulfide bridges

(R)-S-H + H-S-(R') (R)-S-S-(R') + 2 H⁺ + 2 e^-

Chapter 4

Structure of Proteins

Primary

Sequence of amino acid residues.

Secondary

3-Dimensional arrangement of protein backbone.

Tertiary

3-Dimensional arrangement of backbone and side chains (all atoms in chain).

Quaternary

Relationship between interacting polypeptide chains.

Interatomic Forces - determine which of these forces are present at each structure level.

• Covalent bonds (includes peptide bond and disulfide bridge)
• H-bonding (requires X-H, where X = F, O, or N)
• Electrostatic forces (attraction between electrically charges species)
• van der Waal's attractions (attraction between non-polar species)

Denaturing Proteins

Proteins can be denatured ("unfolded") using any one or combination of the following. Several of these act by attempting to strengthen the interaction of the protein with the solution, ultimately resulting in a situation where protein-solution forces are stronger, and thus more stable, than the protein-protein forces.

• heat
• changing pH
• detergents
• molecules that interfere with H-bonding
• reducing agents (used to break apart disulfide bridges).

Identify similarities and differences between -helices and -sheets.

Collagen: -[X-Pro-Gly]-_n triple helix structure. Strands strengthened by hydroxylation.

Myoglobin and Hemoglobin

Hemoglobin and myoglobin are responsible for the transport (H) and storage (M) of oxygen in the body. Be able to identify the important similarities and differences between myoglobin and hemoglobin.
(Primary structure, secondary structure, shape of protein, size of compounds, prosthetic groups, function, O₂ binding strength, etc.).

Know how each of the following factors influence O₂ binding of hemoglobin:

• pH (Increasing concentration of [H+] decreases ability to bind O₂).
• [CO₂] (Addition of CO₂ lowers pH, and therefor decreases ability to bind O₂).
• [BPG] = 2,3-bisphosphoglycerate. (Decreases ability to bind O₂ due to a structural change. Fetal hemoglobin has fewer positively charge sites to interact with BPG, which results in a less BPG and strong O₂ binding).

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Last modified February 5, 1997
Kent State University - Stark Campus
Department of Chemistry
Dr. Clarke Earley